Question: Visualisation Plugin - Icon is not visible
gravatar for sureshhewabi
2.7 years ago by
sureshhewabi20 wrote:



I am new to galaxy and trying to develop a visualisation plugin. I have downloaded a local galaxy.

1) I have config galaxy.ini file:

admin_users =

visualization_plugins_directory = config/plugins/visualizations

2) changed datatypes_conf.xml.sample to datatypes_conf.xml

3) Created folder structure under config/plugins/visualizations

     folder name (protviewer), xml name (protviewer.xml) and mako(protviewer.mako) names are same

4) created config file protviewer.xml

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="ProtViewer">
            <test type="isinstance" test_attr="datatype" result_type="datatype">tabular.Tabular</test>
            <to_param param_attr="id">dataset_id</to_param>
        <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
    <entry_point entry_point_type="mako">protviewer.mako</entry_point>

5) Created protviewer.mako file (for testing purpose I have only basic HTML)

<!DOCTYPE html>
<title>Page Title</title>

<h1>This is a Heading</h1>
<p>This is a paragraph.</p>
<h2>${hda.dataset.datatype} | ${}</h2>


Output of console

galaxy.web.base.pluginframework INFO 2016-03-02 08:09:22,836 VisualizationsRegistry, loaded plugin: charts

galaxy.visualization.plugins.config_parser INFO 2016-03-02 08:09:22,838 Visualizations plugin disabled: Circster. Skipping...

galaxy.visualization.plugins.config_parser INFO 2016-03-02 08:09:22,845 template syntax is deprecated: use entry_point instead

galaxy.web.base.pluginframework INFO 2016-03-02 08:09:22,845 VisualizationsRegistry, loaded plugin: csg

galaxy.web.base.pluginframework INFO 2016-03-02 08:09:22,848 VisualizationsRegistry, loaded plugin: graphview

galaxy.visualization.plugins.config_parser INFO 2016-03-02 08:09:22,850 template syntax is deprecated: use entry_point instead

galaxy.web.base.pluginframework INFO 2016-03-02 08:09:22,850 VisualizationsRegistry, loaded plugin: graphviz

galaxy.web.base.pluginframework INFO 2016-03-02 08:09:22,853 VisualizationsRegistry, loaded plugin: phyloviz

galaxy.web.base.pluginframework INFO 2016-03-02 08:09:22,854 VisualizationsRegistry, loaded plugin: protviewer

galaxy.web.base.pluginframework INFO 2016-03-02 08:09:22,856 VisualizationsRegistry, loaded plugin: scatterplot

galaxy.visualization.plugins.config_parser INFO 2016-03-02 08:09:22,858 Visualizations plugin disabled: Sweepster. Skipping...

galaxy.web.base.pluginframework INFO 2016-03-02 08:09:22,862 VisualizationsRegistry, loaded plugin: trackster

But still I do not see visualisation icon for tabular format file. Not only my visualisation, other visualisation also not working. Do you have any idea why?



galaxy • 759 views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by sureshhewabi20
gravatar for Hotz, Hans-Rudolf
2.7 years ago by
Hotz, Hans-Rudolf1.8k wrote:


Just double checking, before the visualization expert jump in and answer your question: Are you logged-in? The visualization icon will only show up if you are logged-in.


Regards, Hans-Rudolf

ADD COMMENTlink written 2.7 years ago by Hotz, Hans-Rudolf1.8k


No, I am not logged-in. I am testing in localhost:8080. how can i incorporate login? do i need to connect a database or is there a easy way to test this? Thank you


ADD REPLYlink written 2.7 years ago by sureshhewabi20

In the top (black) bar, there is the tab 'User'. Click on "Register" and create your local account. And then you can log in via the same tab




ADD REPLYlink written 2.7 years ago by Hotz, Hans-Rudolf1.8k

Thank you! It works. Sorry I did not know there is a local database connected. Problem Solved!

ADD REPLYlink written 2.7 years ago by sureshhewabi20
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